The metabolism of inorganic nitrogen compounds (see Fig. 1) plays many important physiological roles in microorganisms. Denitrification, a process of converting nitrate to nitrous oxide or dinitrogen gas, allows microbes to use alternative electron acceptors to gain energy under oxygen-limiting conditions [1]. Chemolithotrophic nitrification derives energy from the oxidation of ammonia to nitrite [2]. Dissimilatory reduction of nitrate to ammonia under oxygen-limiting conditions serves as a process to dissipate excess reducing power [3], generates ammonia for assimilation, or supports anaerobic growth with nitrate or nitrite as the alternative electron acceptors [4]. The newly discovered anaerobic ammonia oxidation (anammox) reaction converts ammonium and nitrite to dinitrogen gas (see Fig. 2). Although it is not the subject of this review, microbial nitrogen fixation converts gaseous dinitrogen to ammonia for assimilation. In addition, reactions involving inorganic nitrogen species provide a rich variety of enzymatic systems for biochemical study [5].